Summary of current molecular databases

2006 ◽  
pp. 149-158 ◽  
Author(s):  
W. H. Parkinson
Keyword(s):  
Molecular Databases

scholarly journals Testing temporal changes in allele frequencies: a simulation approach

2010 ◽  
Vol 92 (4) ◽  
pp. 309-320 ◽  
Author(s):  
EDSON SANDOVAL-CASTELLANOS
Keyword(s):  
Molecular Data ◽  
Temporal Changes ◽  
Allele Frequencies ◽  
Small Populations ◽  
Simulation Approach ◽  
Simulation Test ◽  
Agent Based ◽  
Binomial Sampling ◽  
Molecular Databases ◽  
Parameter Values

SummaryAnalysis of the temporal variation in allele frequencies is useful for studying microevolutionary processes. However, many statistical methods routinely used to test temporal changes in allele frequencies fail to establish a proper hypothesis or have theoretical or practical limitations. Here, a Bayesian statistical test is proposed in which the distribution of the distances among sampling frequencies is approached with computer simulations, and hypergeometric sampling is considered instead of binomial sampling. To validate the test and compare its performance with other tests, agent-based model simulations were run for a variety of scenarios, and two real molecular databases were analysed. The results showed that the simulation test (ST) maintained the significance value used (α=0·05) for a vast combination of parameter values, whereas other tests were sensitive to the effect of genetic drift or binomial sampling. The differences between binomial and hypergeometric sampling were more complex than expected, and a novel effect was described. This study suggests that the ST is especially useful for studies with small populations and many alleles, as in microsatellite or sequencing molecular data.

scholarly journals BASECOL2020 New Technical Design

Atoms ◽  
2020 ◽  
Vol 8 (4) ◽  
pp. 69 ◽  
Author(s):  
Yaye-Awa Ba ◽  
Marie-Lise Dubernet ◽  
Nicolas Moreau ◽  
Carlo Maria Zwölf
Keyword(s):  
Interstellar Medium ◽  
Data Center ◽  
Molecular Data ◽  
International Standards ◽  
Rate Coefficients ◽  
Collisional Excitation ◽  
Excitation Rate ◽  
Single Location ◽  
Molecular Databases ◽  
Key Features

The BASECOL database has been created and scientifically enriched since 2004. It contains collisional excitation rate coefficients of molecules for application to the interstellar medium and to cometary atmospheres. Recently, major technical updates have been performed in order to be compliant with international standards for management of data and in order to provide a more friendly environment to query and to present the data. The current paper aims at presenting the key features of the technical updates and to underline the compatibility of BASECOL database with the Virtual Atomic and Molecular Data Center. This latter aims to interconnect atomic and molecular databases, thus providing a single location where users can access atomic and molecular data.

Applications of Bio-molecular Databases in Bioinformatics

2016 ◽  
pp. 329-351 ◽  
Author(s):  
Archana Kumari ◽  
Swarna Kanchan ◽  
Rajeshwar P. Sinha ◽  
Minu Kesheri
Keyword(s):  
Molecular Databases

scholarly journals Emerging Screening Approaches in the Development of Nrf2–Keap1 Protein–Protein Interaction Inhibitors

2019 ◽  
Vol 20 (18) ◽  
pp. 4445 ◽  
Author(s):  
Chung-Hang Leung ◽  
Jia-Tong Zhang ◽  
Guan-Jun Yang ◽  
Hao Liu ◽  
Quan-Bin Han ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Protein Interaction ◽  
Developmental Process ◽  
Protein Protein Interaction ◽  
Lead Compounds ◽  
Disease Therapy ◽  
Molecular Databases ◽  
Viable Approach ◽  
Nrf2 Protein ◽  
Screening Approaches

Due to role of the Keap1–Nrf2 protein–protein interaction (PPI) in protecting cells from oxidative stress, the development of small molecule inhibitors that inhibit this interaction has arisen as a viable approach to combat maladies caused by oxidative stress, such as cancers, neurodegenerative disease and diabetes. To obtain specific and genuine Keap1–Nrf2 inhibitors, many efforts have been made towards developing new screening approaches. However, there is no inhibitor for this target entering the clinic for the treatment of human diseases. New strategies to identify novel bioactive compounds from large molecular databases and accelerate the developmental process of the clinical application of Keap1–Nrf2 protein–protein interaction inhibitors are greatly needed. In this review, we have summarized virtual screening and other methods for discovering new lead compounds against the Keap1–Nrf2 protein–protein interaction. We also discuss the advantages and limitations of different strategies, and the potential of this PPI as a drug target in disease therapy.

Ultrafast shape recognition for similarity search in molecular databases

2007 ◽  
Vol 463 (2081) ◽  
pp. 1307-1321 ◽  
Author(s):  
Pedro J Ballester ◽  
W. Graham Richards
Keyword(s):  
Biological Activity ◽  
Three Dimensional ◽  
Molecular Shape ◽  
Scientific Disciplines ◽  
Distance Distributions ◽  
Molecular Databases ◽  
Hard Problems ◽  
Data Explosion ◽  
Novel Drug ◽  
Drug Leads

Molecular databases are routinely screened for compounds that most closely resemble a molecule of known biological activity to provide novel drug leads. It is widely believed that three-dimensional molecular shape is the most discriminating pattern for biological activity as it is directly related to the steep repulsive part of the interaction potential between the drug-like molecule and its macromolecular target. However, efficient comparison of molecular shape is currently a challenge. Here, we show that a new approach based on moments of distance distributions is able to recognize molecular shape at least three orders of magnitude faster than current methodologies. Such an ultrafast method permits the identification of similarly shaped compounds within the largest molecular databases. In addition, the problematic requirement of aligning molecules for comparison is circumvented, as the proposed distributions are independent of molecular orientation. Our methodology could be also adapted to tackle similar hard problems in other fields, such as designing content-based Internet search engines for three-dimensional geometrical objects or performing fast similarity comparisons between proteins. From a broader perspective, we anticipate that ultrafast pattern recognition will soon become not only useful, but also essential to address the data explosion currently experienced in most scientific disciplines.

scholarly journals The Spectroscopic Atomic and Molecular Databases at the Paris Observatory

Atoms ◽  
2020 ◽  
Vol 8 (3) ◽  
pp. 36 ◽  
Author(s):  
Evelyne Roueff ◽  
Sylvie Sahal-Bréchot ◽  
Milan S. Dimitrijević ◽  
Nicolas Moreau ◽  
Hervé Abgrall
Keyword(s):  
Spontaneous Emission ◽  
Charged Particles ◽  
Oscillator Strengths ◽  
Current Status ◽  
Stark Broadening ◽  
Comprehensive Overview ◽  
Molecular Databases ◽  
Different Temperatures

This paper is intended to give a comprehensive overview of the current status and developments of the Paris Observatory STARK-B, MOLAT and SESAM databases which can be interrogated thanks to interoperability tools. The STARK-B database provides shifting and broadening parameters of different atomic and ionic transitions due to impacts with charged particles (the so-called Stark broadening) for different temperatures and densities. The spectroscopic MOLAT and SESAM databases provide the wavelengths, the oscillator strengths or Einstein spontaneous emission coefficients of H 2 , CO and isotopologues molecules.

Molecular databases on the internet

1997 ◽  
Vol 75 (9) ◽  
pp. 620-623 ◽  
Author(s):  
Martin Ebeling ◽  
Sandor Suhai
Keyword(s):  
The Internet ◽  
Molecular Databases
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